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Prokaryotic Microbial Diversity

Prokaryotic Microbial Diversity. Early attempts at taxonomy: all plants and animals Whitaker scheme (late 20th century): Five kingdoms Animalia, Plantae, Fungi, Protista, and Monera Monera comprised of prokaryotes Classification of bacteria difficult

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Prokaryotic Microbial Diversity

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  1. Prokaryotic Microbial Diversity • Early attempts at taxonomy: all plants and animals • Whitaker scheme (late 20th century): Five kingdoms • Animalia, Plantae, Fungi, Protista, and Monera • Monera comprised of prokaryotes • Classification of bacteria difficult • Plants, animals can be distinguished from each other by physical characteristics; backed up by DNA • Bacteria look very similar • Convergent evolution a problem • Unrelated bacteria develop similar physical and biochemical traits

  2. Goal: Evolutionary classification • In order to understand relatedness, organisms must be viewed at the DNA level • Similar sequences, mutations should give clues • Which genes? Bacteria readily swap genes around. • Carl Woese and 16S RNA • Ribosomal RNA genes cannot afford to mutate much • Changes would interfere with protein synthesis • Change in rRNA genes over time very gradual • Useful for looking at large differences among organisms

  3. Domains • Sequencing rRNA genes reveal differences • Bacteria, Archaea, Eukarya all different from each other • Despite Bacteria, Archaea both being prokaryotes • Differences in Bacteria, Archaea backed up • Aspects of molecular biology • Membrane lipid chemistry • Cell wall chemistry • Extreme environments www.steve.gb.com/science/transcription.html

  4. What’s a Species? • Eukaryotes: plants and animals • Generally, 2 organisms are of same species if they can successfully interbreed • Definition based on sexual reproduction • Bacteria don’t reproduce sexually • Bacterial species: a group of strains that are more closely related to each other than to another group. • Members of a species have DNA that can hybridize • Because of gene exchange, mutation, phase variation, there are no sharp boundaries between species.

  5. Viable, non-culturable bacteria • Many bacteria present in environments: • Do not grow when placed in conventional media • include known pathogenic bacteria • Include bacteria previously unknown • Do not appear to multiply, but many can be shown to be metabolically active • We just don’t know how to grow them? • Pathogenic forms can resume growing in infection • Others…? • Detected and studied using molecular techniques

  6. Metagenomics • Mixed population studies • Using molecular techniques (PCR, sequencing) we find various unique DNA sequences • Most of these bacteria have not/ cannot be cultured • Using molecular techniques to classify unculturable bacteria is called metagenomics • Identification techniques can be molecular or traditional • Traditional techniques require isolation into pure culture, biochemical tests, sometimes serological tests.

  7. Classical and MolecularTaxonomy • Identification by phenotypic analysis • Shape, size, Gram stain • Basic metabolism (aerobic, fermentative, autotrophic) • Motility, pigments, metabolic products, usable carbon sources, temperature range • ID by examining chemical features • Fatty acid composition (FAME) • DNA-DNA hybridization • Ribotyping (specific rRNA sequences; uses PCR) • Multilocus sequence typing (sequences from several conserved genes; uses PCR)

  8. Major groups of Bacteria-1 • Hyperthermophilic Gram negatives • Grow at >70 degrees • Green Sulfur and Green Non-sulfur bacteria • Photosynthetic, anoxygenic • Sulfur bacteria use H2S as electron donor • Deinococcus and relatives • Highly radiation resistant; great DNA repair • Gram negative or positive? Odd mixture of traits • Cyanobacteria • “blue-green algae”; oxygenic photosynthesis

  9. Major groups of Bacteria-2 • Proteobacteria • Largest group of Gram negative bacteria • Enteric bacteria (E.coli, Salmonella, Shigella) • Vibrio (related to enterics; V. cholerae; curved rods) • Pseudomonads (strictly respiratory) • Various groups affecting N and sulfur cycles • Purple sulfur and Purple non-sulfur anoxygenic phototrophs • Rickettsia: obligate intracellular parasites • Bacteroides and Cytophaga • First is strict anaerobic; 2nd aerobic and gliding

  10. Major groups of Bacteria-3 • Gram Positive bacteria • Endospore formers (Bacillus, Clostridium) • Cocci (Staph, Strep, Micrococcus) • Other rods (Mycobacteria, Listeria, etc.) • Actinomycetes (filamentous, antibiotic producers) • Mycoplasma (DNA says G+, but no cell wall) • Spirochetes • Tight spirals, internal flagella, G- • Chlamydia • Obligate intracellular parasites; 2 stage life cycle

  11. Archaea • Methanogens and Halophiles • Methanogens strict anaerobes, make methane • Halophiles need at least 1.5 M salt • Mostly hyperthermophiles • Growth from 80 upwards to 120 degrees C • Third major group has one species!

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